Conformational Changes of the Alanine Dipeptide in Water–Ethanol Binary Mixtures

Almeida, Glauco G.; Cordeiro, João Manuel Marques; Martı́n, M. Elena; Aguilar, M.

doi:10.1021/acs.jctc.5b00952

Cited by 10 publications

(10 citation statements)

References 82 publications

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“…This term, DV, can be evaluated by applying the harmonic oscillator and rigid rotor approximations to the vibrational and rotational modes of the solute in solution, and it needs the information provided by the Hessian matrix, something that makes its calculation difficult in solution systems. In a previous study 72 it was found that the contribution of this term to the conformational equilibrium of a small dipeptide was lower than 0.1 eV. In pCE À we find a similar value.…”

Section: Methods and Computational Detailssupporting

confidence: 80%

“…Oscillator strengths were calculated using the RASSI algorithm implemented in Molcas-7.4. 65 Solvent effects were introduced using the averaged solvent electrostatic potential from the molecular dynamics data (ASEP/MD) method [69][70][71][72][73][74] developed in our laboratory. The method permits combining the quantum-mechanical description of the solute with the microscopic description of the environment.…”

Section: Methods and Computational Detailsmentioning

confidence: 99%

“…Details of the method can be found elsewhere. [69][70][71][72][73][74] Briefly, the solvent perturbation is calculated from classical molecular dynamics (MD) simulations, using a rigid body approximation for the solute geometry and a non-polarizable force field. From the resulting simulation data, the average electrostatic potential generated by the solvent on the solute (ASEP) is obtained.…”

Section: Methods and Computational Detailsmentioning

confidence: 99%

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Solvent effects on de-excitation channels in the p-coumaric acid methyl ester anion, an analogue of the photoactive yellow protein (PYP) chromophore

García-Prieto

Muñoz-Losa

Sánchez

et al. 2016

Phys. Chem. Chem. Phys.

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In an attempt to shed light on the environmental effects on the deactivation channels of the PYP chromophore, radiative and non-radiative deactivation mechanisms of the anionic p-coumaric acid methyl ester (pCE) in the gas phase and water solution are compared at the CASPT2//CASSCF/cc-pVDZ level and, when necessary, at the CASPT2//CASPT2/cc-pVDZ level. We find that the solvent produces dramatic modifications on the free energy profile of the S1 state. Two twisted structures that are minima in the gas phase could not be localized in aqueous solution. Furthermore, the relative stability of minima and conical intersections (CIs) is reverted with respect to the gas phase values, affecting the prevalent de-excitation paths. As a consequence of these changes, three competitive de-excitation channels are open in aqueous solution: the fluorescence emission from a planar minimum on S1, the trans-cis photoisomerization through a CI that involves the rotation of the vinyl double bond and the non-radiative, non-reactive, de-excitation through the CI associated with the rotation of the single bond adjacent to the phenyl group. In the gas phase, the minima are the structures with lower energy, while in solution the CI structure, characterized by a large charge separation, is strongly stabilized by interactions with water molecules and becomes the structure with the lowest energy on S1. These facts explain the low fluorescence signal of pCE in aqueous solution and the presence of partial trans-cis photoisomerization in this system.

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Section: Methods and Computational Detailssupporting

confidence: 80%

Section: Methods and Computational Detailsmentioning

confidence: 99%

Section: Methods and Computational Detailsmentioning

confidence: 99%

See 1 more Smart Citation

Solvent effects on de-excitation channels in the p-coumaric acid methyl ester anion, an analogue of the photoactive yellow protein (PYP) chromophore

García-Prieto

Muñoz-Losa

Sánchez

et al. 2016

Phys. Chem. Chem. Phys.

Self Cite

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“…The radial distribution function (RDF), denoted g(r), is a measure of the probability of finding two atoms at a distance r from each other. This parameter is recurrent in MD trajectory analysis, including in other systems [49][50][51][52]. Its mathematical expression can be written as follows: is the total volume of the system.…”

Section: Structural Propertiesmentioning

confidence: 99%

Water's behaviour on Ca-rich tricalcium silicate surfaces for various degrees of hydration: A molecular dynamics investigation

Claverie

Bernard

Cordeiro

et al. 2019

Journal of Physics and Chemistry of Solids

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To cite this version:J. Claverie, Fabrice Bernard, J.M.M. Cordeiro, Siham Kamali-Bernard. Water's behaviour on Carich tricalcium silicate surfaces for various degrees of hydration A molecular dynamics investigation. AbstractTricalcium silicate (C 3 S) hydration is a highly relevant topic toward a better understanding of ordinary Portland cement. Molecular Dynamics (MD) simulations can provide relevant information about water behaviour at interface with mineral surfaces. For the first time, the influence of C 3 S protonation on water structure and dynamics is assessed by simulating the Ca-rich (040) surface in contact with water. The recently extended INTERFACE force field for C 3 S, including parameters for hydroxyl and silanol groups, was used to perform classical MD calculations. The water layered structure arising from strong hydrogen bonding with the mineral surface decays with increasing hydration of the first atomic layer. We found that the presence of hydroxyl and silanol groups, as well as desorption of calcium cations strongly influence the structural and dynamical properties of water.

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“…More recently, in a QM/MM study devoted to understand the conformational behavior of the alanine dipeptide in ethanol-water mixtures it is shown that in contrast to the results in water, the αR conformation exhibits lower energy than the PII conformation in ethanol [29].…”

Section: Introductionmentioning

confidence: 99%

Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations

Rubio-Martínez

Tomás

Pérez

2017

Journal of Molecular Graphics and Modelling

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This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Graphical abstract Highlights The manuscript describes a computational study of the differential conformational behavior of the alanine dipeptide in diverse solvents including chloroform, methanol, DMSO, water and methyl formamide.  This study is important to understand the conformational behavior of peptides in diverse solvents, since the dialanine dipeptide is a model molecule to for peptides.  The manuscript discusses the role of inter-and intra-molecular interactions to understand the differential behavior of the molecule in the diverse solvents.2  This work aims to shed light into the controversy found in the literature between experimental and theoretical calculations of the dialanine dipeptide in water.  There has never been published a comparative computational study of the effect of the solvent on the molecule. AbstractIn general, peptides do not exhibit a well-defined conformational profile in solution. However, despite the experimental blurred picture associated with their structure, compelling spectroscopic evidence shows that peptides exhibit local order. The conformational profile of a peptide is the result of a balance between intramolecular interactions between different atoms of the molecule and intermolecular interactions between atoms of the molecule and the solvent. Accordingly, the conformational profile of a peptide will change upon the properties of the solvent it is soaked. To get insight into the balance between intra-and intermolecular interactions on the conformational preferences of the peptide backbone we have studied the conformational profile of the alanine dipeptide in diverse solvents using molecular dynamics as sampling technique. Solvents

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Conformational Changes of the Alanine Dipeptide in Water–Ethanol Binary Mixtures

Cited by 10 publications

References 82 publications

Solvent effects on de-excitation channels in the p-coumaric acid methyl ester anion, an analogue of the photoactive yellow protein (PYP) chromophore

Solvent effects on de-excitation channels in the p-coumaric acid methyl ester anion, an analogue of the photoactive yellow protein (PYP) chromophore

Water's behaviour on Ca-rich tricalcium silicate surfaces for various degrees of hydration: A molecular dynamics investigation

Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations

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